[BioC] Repeated Measures mRNA expression analysis

Mike Love michaelisaiahlove at gmail.com
Tue Jun 25 08:00:42 CEST 2013

Hi Charles,

On Jun 24, 2013, at 10:08 PM, Charles Determan Jr <deter088 at umn.edu> wrote:

> design(dds) <- formula(~ time + treatment)
> Is this what is considered the appropriate way to address repeated measures
> in mRNA expression experiments?  Any thoughts are appreciated.

Yes, this is the correct design formula for DESeq2 for estimating and testing the effect of treatment over all time points. We use by default a Wald test, and the likelihood ratio test is also implemented (see vignette). This is then a similar approach to calling anova.glm() on a glm fit for a single gene.



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